Alignments for a candidate for serC in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Trichormus variabilis ATCC 29413

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_011318017.1 AVA_RS05940 phosphoserine transaminase

Query= metacyc::MONOMER-15918
         (370 letters)



>NCBI__GCF_000204075.1:WP_011318017.1
          Length = 392

 Score =  467 bits (1202), Expect = e-136
 Identities = 228/378 (60%), Positives = 282/378 (74%), Gaps = 10/378 (2%)

Query: 3   PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62
           PT  P+   FSSGPCAKHPG+SV  L++   GRSHRS+ GK KL+E I+R++ +LGLP D
Sbjct: 8   PTNKPQVTHFSSGPCAKHPGWSVSNLENACLGRSHRSEDGKAKLSEVIERSKQILGLPAD 67

Query: 63  YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122
           Y +GIVPASDTGA EM LWS+LG R +D+L WESF + W  D+  +LKL D R+ +A YG
Sbjct: 68  YRLGIVPASDTGAVEMALWSLLGQRPLDILAWESFGQEWVKDVVDELKLPDVRLLKAPYG 127

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182
            LP+L +VDF +DVVF+WNGTTSGV+VPN DWI DDR+G+T+CDATSA+FAMDIP+ K+D
Sbjct: 128 GLPNLDEVDFSHDVVFLWNGTTSGVRVPNGDWIKDDRQGLTICDATSAVFAMDIPWEKID 187

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242
           V+T+SWQKVLGGE  HG+++LSPRAV+RL++Y PAWP+PKIFRL++ GKL + IF G TI
Sbjct: 188 VLTYSWQKVLGGEAQHGVIVLSPRAVERLQTYEPAWPIPKIFRLSQKGKLIEGIFKGDTI 247

Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSML  ED L  L WAESVGGL  LI R+  NLA    +V ++NW  FLAE  E RS 
Sbjct: 248 NTPSMLCVEDALDALIWAESVGGLPGLISRSEANLAAIAQWVKQSNWADFLAEKPETRSC 307

Query: 303 TSVCFKV------DLSDEK----LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352
           TS+C K+       LS E      K+L K LEK++VAYDI  YR AP GLRIW GATVE 
Sbjct: 308 TSICLKIVDAAFASLSAEDQGKFAKKLAKLLEKQQVAYDIAPYRAAPPGLRIWGGATVET 367

Query: 353 EDLECLCEWIEWAYNLVK 370
            D+E L  W++WAY  VK
Sbjct: 368 ADIEALLPWLDWAYANVK 385


Lambda     K      H
   0.319    0.136    0.430 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 501
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 370
Length of database: 392
Length adjustment: 30
Effective length of query: 340
Effective length of database: 362
Effective search space:   123080
Effective search space used:   123080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011318017.1 AVA_RS05940 (phosphoserine transaminase)
to HMM TIGR01365 (phosphoserine aminotransferase (EC 2.6.1.52))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01365.hmm
# target sequence database:        /tmp/gapView.15503.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01365  [M=374]
Accession:   TIGR01365
Description: serC_2: phosphoserine aminotransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-193  627.3   0.3   5.6e-193  627.0   0.3    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011318017.1  AVA_RS05940 phosphoserine transa


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011318017.1  AVA_RS05940 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.0   0.3  5.6e-193  5.6e-193       2     373 ..      12     383 ..      11     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 627.0 bits;  conditional E-value: 5.6e-193
                                 TIGR01365   2 panpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtga 70 
                                               p+  +fssgpcak+pg+sv +l na lgrshrs+ gk+kl e ie+++++l++pady++giv+asdtga
  lcl|NCBI__GCF_000204075.1:WP_011318017.1  12 PQVTHFSSGPCAKHPGWSVSNLENACLGRSHRSEDGKAKLSEVIERSKQILGLPADYRLGIVPASDTGA 80 
                                               77789**************************************************************** PP

                                 TIGR01365  71 vemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngtt 139
                                               vemalwsllg+r++d+la+esfg++wv dv+ +lkl+dvr l+a+yg lp+l  vdf++dvvf wngtt
  lcl|NCBI__GCF_000204075.1:WP_011318017.1  81 VEMALWSLLGQRPLDILAWESFGQEWVKDVVDELKLPDVRLLKAPYGGLPNLDEVDFSHDVVFLWNGTT 149
                                               ********************************************************************* PP

                                 TIGR01365 140 sgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarles 208
                                               sgvrvpngd+i +dr+glticdatsa+fa+d+++ek+dv+t+swqkvlgge  hgv++lsprav+rl++
  lcl|NCBI__GCF_000204075.1:WP_011318017.1 150 SGVRVPNGDWIKDDRQGLTICDATSAVFAMDIPWEKIDVLTYSWQKVLGGEAQHGVIVLSPRAVERLQT 218
                                               ********************************************************************* PP

                                 TIGR01365 209 ytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavlea 277
                                               y+pawp+pkifrl++ gkl+++if+g+tintpsml+vedaldal waes+ggl  l++r+++nla +++
  lcl|NCBI__GCF_000204075.1:WP_011318017.1 219 YEPAWPIPKIFRLSQKGKLIEGIFKGDTINTPSMLCVEDALDALIWAESVGGLPGLISRSEANLAAIAQ 287
                                               ********************************************************************* PP

                                 TIGR01365 278 fvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapag 346
                                               +v++s+w dfla+++e+rs ts+clk+vd + a l ++ q +fak+l+++lek++vaydi  yr ap+g
  lcl|NCBI__GCF_000204075.1:WP_011318017.1 288 WVKQSNWADFLAEKPETRSCTSICLKIVDAAFASLSAEDQGKFAKKLAKLLEKQQVAYDIAPYRAAPPG 356
                                               ********************************************************************* PP

                                 TIGR01365 347 lriwcgatveksdleallewldwafal 373
                                               lriw gatve+ d+eall+wldwa+a 
  lcl|NCBI__GCF_000204075.1:WP_011318017.1 357 LRIWGGATVETADIEALLPWLDWAYAN 383
                                               *************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (392 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.86
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis